Methods for strand displacement amplification of linear templates are well known in the art. In general, methods for strand displacement amplification of linear templates use some kind of process to digest a sequence region at or near the 5′-end of one strand of a double-stranded DNA that has been synthesized using the other strand as a template in order to provide a complementary region for another primer to anneal to the template strand. Once annealed to the template, the primer is then “primer extended” by a DNA polymerase that has strand-displacing activity, thereby displacing the strand in front of the 3′-end of the replicating DNA. This process, which can be thought of as “liberating the primer binding site”, is repeated over and over. Each round of liberating the primer binding site on the template, annealing of another primer and DNA synthesis results in release or “displacement” of the last-synthesized DNA strand.
By way of example, but not of limitation, methods for strand displacement amplification are disclosed in PCT Patent Publication Nos. WO 02/16639; WO 00/56877; and AU 00/29742 of Takara Shuzo Company; U.S. Pat. Nos. 5,523,204; 5,536,649; 5,624,825; 5,631,147; 5,648,211; 5,733,752; 5,744,311; 5,756,702; and 5,916,779 of Becton Dickinson and Company; U.S. Pat. Nos. 6,238,868; 6,309,833; and 6,326,173 of Nanogen/Becton Dickinson Partnership; U.S. Pat. Nos. 5,849,547; 5,874,260; and 6,218,151 of Bio Merieux; U.S. Pat. Nos. 5,786,183; 6,087,133; and 6,214,587 of Gen-Probe, Inc.; U.S. Pat. No. 6,063,604 of Wick et al.; U.S. Pat. No. 6,251,639 and U.S. patent application Ser. 20010034048; 20030017591; 20030087251; and 20030186234 of Kurn; U.S. Pat. No. 6,410,278; and PCT Publication No. WO 00/28082 of Eiken Kagaku Kabushiki Kaishi, Tokyo, Japan; U.S. Pat. Nos. 5,591,609; 5,614,389; 5,773,733; 5,834,202; and 6,448,017 of Auerbach; and U.S. Pat. Nos. 6,124,120; and 6,280,949 of Lizardi, all of which are incorporated herein by reference.
The methods disclosed in U.S. Pat. Nos. 5,523,204; 5,536,649; 5,624,825; 5,631,147; 5,648,211; 5,733,752; 5,744,311; 5,756,702; and 5,916,779 of Becton Dickinson and Company use a restriction enzyme to liberate the primer binding site.
The methods disclosed in U.S. Pat. Nos. 5,786,183; 6,087,133; and 6,214,587 of Gen-Probe, Inc. use multiple primers, typically with a 5′-flap, in the absence of a restriction enzyme to liberate the primer-binding sites. The methods disclosed in U.S. Pat. No. 6,063,604 of Wick et al., use primers designed to have a restriction endonuclease nick site to liberate the primer binding site from the template strand. The methods disclosed by Sagawa et al., in PCT Patent Publication No. WO 02/16639 and in PCT Patent Publications Nos. WO 00/56877 and AU 00/29742 use a composite primer having a 5′-portion comprising deoxyribonucleotides and a 3′-portion comprising ribonucleotides, and then use RNase H to liberate the primer-binding site at the 5′-end. The methods disclosed in U.S. Pat. No. 6,251,639 of Kurn use a composite primer having a 5′-portion comprising ribonucleotides and a 3′-portion comprising deoxyribonucleotides, and then use RNase H to liberate the primer-binding site at the 5′-end of the replicating DNA strand.
While all of these methods result in amplification of single-stranded DNA that is complementary to the template strand, still other methods and kits are needed that are less expensive and that permit easier design of assays for a variety of target sequences.